DNA-binding specificities of plant transcription factors and their potential to define target genes

By J. Franco-Zorrilla, I. López-Vidriero, J. L. Carrasco, Marta Godoy, P. Vera, R. Solano. Proceedings of the National Academy of Sciences of the United States of America, 2014

653 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/cdc2626f240f24c961207b8759cfd345d9f4ca86

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Citations in the corpus

Auxin Response Factors — output control in auxin biology (2017, background): “For example, protein-binding microarrays (PBMs) showed that the original AuxRE was not the sequence with the highest ARF-binding affinity, and instead identified the TGTCGG element as a high-affinity binding site (Boer et al. , 2014; Franco-Zorrilla et al. , 2014).”
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants (2016, methodology): “0) (34)), literature (22) and motifs discovered from ChIPseq peaks using MEME-ChIP (35).”
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework (2017, methodology): “DNA regions at which TFs bind are defined as TF-binding sites (TFBSs) and can be identified in vivo by methods such as chromatin immunoprecipitation (ChIP) or in vitro by methods based on binding of large pools of DNA fragments (e.g. Systematic evolution of ligands by exponential enrichment (SELEX) ”
Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape (2016, neutral): “2014] and 24 from PBM [Franco-Zorrilla et al. 2014]; Figure 2C; Table S1D), we found quantitative agreement between the DAP-seq and PBM-derived PWM (Figure S1C), although the DAP-seq PWM contained a higher number of informative positions (information content R 0.”
Transcription Factors and Plants Response to Drought Stress: Current Understanding and Future Directions (2016, neutral): “As illustrated in Figure 1 , TFs regulate gene expression through binding to cis -regulatory elements in the promoter region of diﬀerent stress-related genes (Nuruzzaman et al., 2013; Franco-Zorrilla et al., 2014).”
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework (2017, methodology): “DNA regions at which TFs bind are defined as TF-binding sites (TFBSs) and can be identified in vivo by methods such as chromatin immunoprecipitation (ChIP) or in vitro by methods based on binding of large pools of DNA fragments (e.g. Systematic evolution of ligands by exponential enrichment (SELEX) ”